User:Wayne Decatur/Biochem642 Molecular Visualization 2010 Fall Sessions

Introduction

 * Logistical information about class today and next week and problem sets
 * Importance of Structural Biology
 * Important for understanding function
 * helpful representations and models for people learning
 * Nobel prizes 2009 studies of the structure and function of the ribosome structure.

Structural Biology for Non-structural Biologists

 * MolviZ "Top 5"
 * items III-V pertinent today
 * particularly item III shows us how we can explore structures.
 * Proteopedia - interactive 3D encylopedia of macromolecular structures and structural biology resources to which scientists contribute and use to share structural biology content
 * Proteopedia allows sharing of structural biology data in a 3D, interactive manner
 * Plant Viral Protein p19 Suppression of RNA Silencing
 * The Glutamate Receptor (GluA2)
 * Resources and information
 * About Macromolecular Structure
 * Searching
 * 2 means - example search net charge


 * Proteopedia has an entry for every PDB entry with links to useful items
 * PDB 4 digit alphanumeric accession number, similar to a PubMed ID or Genbank sequence accession number
 * Conservation: 5cyt, explanation, and see also The ConSurf Database and The ConSurf Server (Note: This is also item IV at MolviZ "Top 5".)
 * RCSB = Protein Data Bank - use link under 5cyt to RCSB

Protein Data Bank

 * X-ray crystallography, NMR, and cryo-EM structures - total 68,840
 * From FAQ: "Since October 15, 2006, PDB depositions have been restricted to atomic coordinates that are substantially determined by experimental measurements on specimens containing biological macromolecules."
 * Slide on overview of crystallography, NMR, and cryo-EM structures
 * I'll point you to Eric Martz's recent workshop if you seek more information in 3D-interactive examples on on resolution, temperature (b-factors, and electron density maps.
 * Display PDB file of 1d66 - just a useful example of DNA-binding by a transcription factor and protein used in fusions in many genomic screens
 * Under 'Links' go to Proteopedia entry for 1d66
 * Open 'FirstGlance' under 'Resources' for 1d66

FirstGlance in Jmol

 * Views and Convenience buttons
 * How many chains?
 * Hover (special to FirstGlance is ability to click and display identity; hover more general in Jmol. Model number would be shown if more than 1.)(Another trick to see if ligand is part of a chain is to use Proteopedia's Scene Authoring Tools and limit to chain and represent as ball and stick because covalent linkages will clearly be shown.)
 * N→C Rainbow (HELP PANE)
 * Charge/Hydrophobic with Slab on/off. Where are the Ligands? Be aware when Ligands are on or off; ligands are often interesting moieties in the structure.
 * Center atom
 * Gaps - I'd suggest helpful PDBSum linked to at Proteopedia vs. less clear Sequence at PDB or S2C (compare 2ace)
 * More Views
 * Distance measuring
 * Contacts

Proteopedia Scene Authoring

 * Perform basic editing and creation of scenes in your Sandboxes

Time permitting

 * Proteopedia pages can be exported for offline viewing using the toolbox on the left.
 * Pymol to Jmol conversion built into Proteopedia's Scene Authoring Tools
 * Item V on MolviZ "Top 5" - Polyview-3D = fancy PyMol views and animations made super easy via a web server with forms.
 * Morphing allows displaying the visual transition between two molecular conformations.

Molecular Visualization

 * About Macromolecular Structure
 * Proteopedia - a scientific 'wiki' bridging the rift between 3D structure and function of biomacromolecules, Eran Hodis, Jaime Prilusky, Eric Martz, Israel Silman, John Moult and Joel L Sussman. Genome Biology 9:R121, August 2008 or doi:10.1186/gb-2008-9-8-r121
 * MolviZ "Top 5"
 * MolviZ.Org
 * Protein Explorer's Glossary
 * Eric Martz's recent workshop at his list of workshops.
 * Jmol Application
 * PyMol
 * Polyview-3D, fancy PyMol views and animations made super easy via a web server with forms.
 * Swiss-pdb Viewer a.k.a Deep View
 * Protein Explorer

Authoring Scenes and Views in Proteopedia and beyond

 * Proteopedia:Video Guide
 * Proteopedia:How to Make a Page
 * How to edit pages in Proteopedia → Example 1, example 2, and example 3 of edited topic pages.
 * Special:Upload List of allowed file types: png, jpg, jpeg, tiff, tif, gif, mgif, pdb, cif, mmcif, cml, mol, xyz, kin, mmol
 * Proteopedia's Scene Authoring Tools
 * Perform basic editing and creation of scenes in your Sandboxes
 * Copying FirstGlance Scenes into Proteopedia
 * Proteopedia pages can be exported for offline viewing using the toolbox on the left.


 * User:Tom Gluick/glutamine synthetase (University of Maryland, Baltimore County). Includes instructions for using Jmol commands in the Jmol console for advanced scene authoring.
 * Jmol Command Reference Manual for advanced scene authoring in Jmol using commands because direct scripting works for Proteopedia too.
 * Comparison of Jmol tutorial-authoring systems
 * Copying FirstGlance in Jmol Scenes into Proteopedia
 * Jmol Protein Explorer's powerful Quickviews approach really helps quickly generate particular scenes or ideas for scenes to generate elsewhere. Using the information detailed here or at the JTAT site on extracting state scripts, it is possible to go from these views to Proteopedia scenes; however, as the version of Jmol differs there may be discrepancies and issues.
 * Jmol Tutorial-Authoring Template (JTAT) describes and works for developing and viewing scenes offline or developing and viewing privately.
 * Morphing allows displaying the visual transition between two molecular conformations.
 * Polyview-3D, fancy PyMol views and animations made super easy via a web server with forms.
 * eMovie,a PyMol plug-in for macromolecular movie-making.